Starting phenix.real_space_refine on Mon Aug 5 08:22:46 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8v49_42969/08_2024/8v49_42969.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8v49_42969/08_2024/8v49_42969.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.62 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8v49_42969/08_2024/8v49_42969.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8v49_42969/08_2024/8v49_42969.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8v49_42969/08_2024/8v49_42969.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8v49_42969/08_2024/8v49_42969.cif" } resolution = 3.62 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.012 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 3 5.49 5 S 48 5.16 5 C 8197 2.51 5 N 2155 2.21 5 O 2431 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "D TYR 271": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 271": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/chem_data/mon_lib" Total number of atoms: 12834 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 3236 Number of conformers: 1 Conformer: "" Number of residues, atoms: 401, 3236 Classifications: {'peptide': 401} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 10, 'TRANS': 390} Chain breaks: 4 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "B" Number of atoms: 3148 Number of conformers: 1 Conformer: "" Number of residues, atoms: 390, 3148 Classifications: {'peptide': 390} Link IDs: {'PTRANS': 9, 'TRANS': 380} Chain breaks: 6 Chain: "D" Number of atoms: 3236 Number of conformers: 1 Conformer: "" Number of residues, atoms: 401, 3236 Classifications: {'peptide': 401} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 10, 'TRANS': 390} Chain breaks: 4 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "C" Number of atoms: 3183 Number of conformers: 1 Conformer: "" Number of residues, atoms: 394, 3183 Classifications: {'peptide': 394} Link IDs: {'PTRANS': 10, 'TRANS': 383} Chain breaks: 6 Chain: "A" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 7.65, per 1000 atoms: 0.60 Number of scatterers: 12834 At special positions: 0 Unit cell: (99.11, 126.225, 169.235, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 48 16.00 P 3 15.00 O 2431 8.00 N 2155 7.00 C 8197 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 4.84 Conformation dependent library (CDL) restraints added in 2.3 seconds 3076 Ramachandran restraints generated. 1538 Oldfield, 0 Emsley, 1538 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3024 Finding SS restraints... Secondary structure from input PDB file: 67 helices and 12 sheets defined 55.2% alpha, 13.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.42 Creating SS restraints... Processing helix chain 'A' and resid 39 through 51 Processing helix chain 'A' and resid 53 through 60 removed outlier: 3.539A pdb=" N ARG A 56 " --> pdb=" O ASP A 53 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N ALA A 58 " --> pdb=" O ILE A 55 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N LEU A 60 " --> pdb=" O PHE A 57 " (cutoff:3.500A) Processing helix chain 'A' and resid 81 through 85 Processing helix chain 'A' and resid 102 through 110 removed outlier: 3.812A pdb=" N ARG A 110 " --> pdb=" O MET A 106 " (cutoff:3.500A) Processing helix chain 'A' and resid 127 through 138 Processing helix chain 'A' and resid 151 through 159 removed outlier: 3.741A pdb=" N ALA A 157 " --> pdb=" O THR A 153 " (cutoff:3.500A) Processing helix chain 'A' and resid 177 through 189 Processing helix chain 'A' and resid 199 through 237 Processing helix chain 'A' and resid 249 through 264 Processing helix chain 'A' and resid 265 through 269 Processing helix chain 'A' and resid 273 through 287 Processing helix chain 'A' and resid 296 through 319 Processing helix chain 'A' and resid 319 through 331 Processing helix chain 'A' and resid 362 through 366 Processing helix chain 'A' and resid 367 through 380 removed outlier: 3.627A pdb=" N LEU A 373 " --> pdb=" O GLY A 369 " (cutoff:3.500A) Processing helix chain 'A' and resid 399 through 413 removed outlier: 3.670A pdb=" N ASP A 405 " --> pdb=" O ASP A 401 " (cutoff:3.500A) removed outlier: 5.128A pdb=" N LEU A 407 " --> pdb=" O GLN A 403 " (cutoff:3.500A) removed outlier: 5.394A pdb=" N LYS A 408 " --> pdb=" O GLU A 404 " (cutoff:3.500A) Processing helix chain 'A' and resid 425 through 430 removed outlier: 4.108A pdb=" N ALA A 429 " --> pdb=" O SER A 425 " (cutoff:3.500A) Processing helix chain 'A' and resid 432 through 434 No H-bonds generated for 'chain 'A' and resid 432 through 434' Processing helix chain 'B' and resid 13 through 17 removed outlier: 3.729A pdb=" N ARG B 17 " --> pdb=" O ILE B 14 " (cutoff:3.500A) Processing helix chain 'B' and resid 39 through 51 Processing helix chain 'B' and resid 53 through 60 removed outlier: 3.636A pdb=" N ARG B 56 " --> pdb=" O ASP B 53 " (cutoff:3.500A) Processing helix chain 'B' and resid 102 through 110 removed outlier: 3.706A pdb=" N ALA B 107 " --> pdb=" O GLY B 103 " (cutoff:3.500A) Processing helix chain 'B' and resid 127 through 139 Processing helix chain 'B' and resid 151 through 161 Processing helix chain 'B' and resid 175 through 189 Processing helix chain 'B' and resid 199 through 239 removed outlier: 3.621A pdb=" N PHE B 238 " --> pdb=" O PHE B 234 " (cutoff:3.500A) Processing helix chain 'B' and resid 250 through 264 Processing helix chain 'B' and resid 273 through 288 Processing helix chain 'B' and resid 294 through 319 Processing helix chain 'B' and resid 322 through 331 Processing helix chain 'B' and resid 362 through 366 Processing helix chain 'B' and resid 370 through 380 Processing helix chain 'B' and resid 399 through 413 removed outlier: 4.888A pdb=" N LEU B 407 " --> pdb=" O GLN B 403 " (cutoff:3.500A) removed outlier: 4.836A pdb=" N LYS B 408 " --> pdb=" O GLU B 404 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ARG B 409 " --> pdb=" O ASP B 405 " (cutoff:3.500A) Processing helix chain 'D' and resid 39 through 51 Processing helix chain 'D' and resid 53 through 60 removed outlier: 3.548A pdb=" N ARG D 56 " --> pdb=" O ASP D 53 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N ALA D 58 " --> pdb=" O ILE D 55 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N LEU D 60 " --> pdb=" O PHE D 57 " (cutoff:3.500A) Processing helix chain 'D' and resid 81 through 85 Processing helix chain 'D' and resid 102 through 110 removed outlier: 3.815A pdb=" N ARG D 110 " --> pdb=" O MET D 106 " (cutoff:3.500A) Processing helix chain 'D' and resid 127 through 138 Processing helix chain 'D' and resid 151 through 159 removed outlier: 3.547A pdb=" N ALA D 157 " --> pdb=" O THR D 153 " (cutoff:3.500A) Processing helix chain 'D' and resid 177 through 189 Processing helix chain 'D' and resid 199 through 237 Processing helix chain 'D' and resid 249 through 264 Processing helix chain 'D' and resid 265 through 269 Processing helix chain 'D' and resid 273 through 287 Processing helix chain 'D' and resid 296 through 319 Processing helix chain 'D' and resid 319 through 331 Processing helix chain 'D' and resid 362 through 366 Processing helix chain 'D' and resid 367 through 380 removed outlier: 3.580A pdb=" N LEU D 373 " --> pdb=" O GLY D 369 " (cutoff:3.500A) Processing helix chain 'D' and resid 399 through 413 removed outlier: 3.691A pdb=" N ASP D 405 " --> pdb=" O ASP D 401 " (cutoff:3.500A) removed outlier: 5.135A pdb=" N LEU D 407 " --> pdb=" O GLN D 403 " (cutoff:3.500A) removed outlier: 5.354A pdb=" N LYS D 408 " --> pdb=" O GLU D 404 " (cutoff:3.500A) Processing helix chain 'D' and resid 425 through 430 removed outlier: 4.068A pdb=" N ALA D 429 " --> pdb=" O SER D 425 " (cutoff:3.500A) Processing helix chain 'D' and resid 432 through 434 No H-bonds generated for 'chain 'D' and resid 432 through 434' Processing helix chain 'C' and resid 39 through 51 Processing helix chain 'C' and resid 53 through 60 removed outlier: 3.565A pdb=" N ARG C 56 " --> pdb=" O ASP C 53 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N ALA C 58 " --> pdb=" O ILE C 55 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N LEU C 60 " --> pdb=" O PHE C 57 " (cutoff:3.500A) Processing helix chain 'C' and resid 102 through 110 removed outlier: 3.884A pdb=" N ARG C 110 " --> pdb=" O MET C 106 " (cutoff:3.500A) Processing helix chain 'C' and resid 127 through 138 Processing helix chain 'C' and resid 151 through 159 removed outlier: 3.721A pdb=" N ALA C 157 " --> pdb=" O THR C 153 " (cutoff:3.500A) Processing helix chain 'C' and resid 178 through 189 Processing helix chain 'C' and resid 199 through 237 Processing helix chain 'C' and resid 250 through 264 Processing helix chain 'C' and resid 273 through 287 Processing helix chain 'C' and resid 294 through 319 removed outlier: 3.637A pdb=" N SER C 298 " --> pdb=" O GLU C 294 " (cutoff:3.500A) Processing helix chain 'C' and resid 319 through 331 Processing helix chain 'C' and resid 362 through 366 Processing helix chain 'C' and resid 367 through 380 Processing helix chain 'C' and resid 399 through 413 removed outlier: 3.553A pdb=" N ASP C 405 " --> pdb=" O ASP C 401 " (cutoff:3.500A) removed outlier: 4.981A pdb=" N LEU C 407 " --> pdb=" O GLN C 403 " (cutoff:3.500A) removed outlier: 5.315A pdb=" N LYS C 408 " --> pdb=" O GLU C 404 " (cutoff:3.500A) Processing helix chain 'C' and resid 425 through 430 removed outlier: 4.023A pdb=" N ALA C 429 " --> pdb=" O SER C 425 " (cutoff:3.500A) Processing helix chain 'C' and resid 432 through 434 No H-bonds generated for 'chain 'C' and resid 432 through 434' Processing sheet with id=AA1, first strand: chain 'A' and resid 98 through 101 removed outlier: 4.025A pdb=" N VAL A 90 " --> pdb=" O ILE A 98 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N PHE A 100 " --> pdb=" O ILE A 88 " (cutoff:3.500A) removed outlier: 7.102A pdb=" N GLU A 64 " --> pdb=" O LEU A 11 " (cutoff:3.500A) removed outlier: 5.304A pdb=" N LEU A 11 " --> pdb=" O GLU A 64 " (cutoff:3.500A) removed outlier: 7.147A pdb=" N LYS A 66 " --> pdb=" O ILE A 9 " (cutoff:3.500A) removed outlier: 5.116A pdb=" N ILE A 9 " --> pdb=" O LYS A 66 " (cutoff:3.500A) removed outlier: 7.018A pdb=" N THR A 68 " --> pdb=" O SER A 7 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N LEU A 20 " --> pdb=" O LEU A 11 " (cutoff:3.500A) removed outlier: 5.476A pdb=" N TYR A 18 " --> pdb=" O LYS A 13 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 146 through 148 removed outlier: 3.764A pdb=" N CYS A 422 " --> pdb=" O ILE A 391 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 337 through 340 Processing sheet with id=AA4, first strand: chain 'B' and resid 20 through 23 removed outlier: 3.863A pdb=" N ILE B 9 " --> pdb=" O VAL B 22 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N GLU B 64 " --> pdb=" O SER B 12 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 29 through 31 removed outlier: 6.589A pdb=" N VAL B 389 " --> pdb=" O ILE B 420 " (cutoff:3.500A) removed outlier: 8.067A pdb=" N CYS B 422 " --> pdb=" O VAL B 389 " (cutoff:3.500A) removed outlier: 7.263A pdb=" N ILE B 391 " --> pdb=" O CYS B 422 " (cutoff:3.500A) removed outlier: 6.496A pdb=" N PHE B 148 " --> pdb=" O ASP B 392 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 338 through 341 Processing sheet with id=AA7, first strand: chain 'D' and resid 98 through 101 removed outlier: 4.317A pdb=" N VAL D 90 " --> pdb=" O ILE D 98 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N PHE D 100 " --> pdb=" O ILE D 88 " (cutoff:3.500A) removed outlier: 6.994A pdb=" N GLU D 64 " --> pdb=" O LEU D 11 " (cutoff:3.500A) removed outlier: 5.229A pdb=" N LEU D 11 " --> pdb=" O GLU D 64 " (cutoff:3.500A) removed outlier: 7.222A pdb=" N LYS D 66 " --> pdb=" O ILE D 9 " (cutoff:3.500A) removed outlier: 5.465A pdb=" N ILE D 9 " --> pdb=" O LYS D 66 " (cutoff:3.500A) removed outlier: 7.447A pdb=" N THR D 68 " --> pdb=" O SER D 7 " (cutoff:3.500A) removed outlier: 4.276A pdb=" N LEU D 20 " --> pdb=" O LEU D 11 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N LYS D 13 " --> pdb=" O TYR D 18 " (cutoff:3.500A) removed outlier: 5.556A pdb=" N TYR D 18 " --> pdb=" O LYS D 13 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 146 through 148 removed outlier: 4.012A pdb=" N CYS D 422 " --> pdb=" O ILE D 391 " (cutoff:3.500A) removed outlier: 7.473A pdb=" N ILE D 437 " --> pdb=" O LEU D 28 " (cutoff:3.500A) removed outlier: 6.271A pdb=" N VAL D 30 " --> pdb=" O ILE D 437 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 337 through 340 removed outlier: 3.788A pdb=" N ALA D 339 " --> pdb=" O GLY D 352 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N GLY D 352 " --> pdb=" O ALA D 339 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 98 through 101 removed outlier: 3.634A pdb=" N PHE C 100 " --> pdb=" O ILE C 88 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ILE C 88 " --> pdb=" O PHE C 100 " (cutoff:3.500A) removed outlier: 6.421A pdb=" N GLU C 64 " --> pdb=" O LEU C 11 " (cutoff:3.500A) removed outlier: 4.597A pdb=" N LEU C 11 " --> pdb=" O GLU C 64 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N LYS C 66 " --> pdb=" O ILE C 9 " (cutoff:3.500A) removed outlier: 4.594A pdb=" N ILE C 9 " --> pdb=" O LYS C 66 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N THR C 68 " --> pdb=" O SER C 7 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N LEU C 20 " --> pdb=" O LEU C 11 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N LYS C 13 " --> pdb=" O TYR C 18 " (cutoff:3.500A) removed outlier: 5.410A pdb=" N TYR C 18 " --> pdb=" O LYS C 13 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 144 through 148 removed outlier: 4.069A pdb=" N GLN C 418 " --> pdb=" O ALA C 387 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ILE C 391 " --> pdb=" O ILE C 420 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N CYS C 422 " --> pdb=" O ILE C 391 " (cutoff:3.500A) removed outlier: 6.139A pdb=" N ASN C 29 " --> pdb=" O VAL C 421 " (cutoff:3.500A) removed outlier: 6.282A pdb=" N VAL C 30 " --> pdb=" O ILE C 437 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 337 through 341 713 hydrogen bonds defined for protein. 2007 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.06 Time building geometry restraints manager: 5.36 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3806 1.34 - 1.46: 2087 1.46 - 1.57: 7076 1.57 - 1.69: 5 1.69 - 1.81: 92 Bond restraints: 13066 Sorted by residual: bond pdb=" C PHE B 355 " pdb=" N PRO B 356 " ideal model delta sigma weight residual 1.335 1.354 -0.019 1.28e-02 6.10e+03 2.20e+00 bond pdb=" CB ILE C 439 " pdb=" CG1 ILE C 439 " ideal model delta sigma weight residual 1.530 1.556 -0.026 2.00e-02 2.50e+03 1.73e+00 bond pdb=" CA ILE C 439 " pdb=" CB ILE C 439 " ideal model delta sigma weight residual 1.535 1.550 -0.015 1.18e-02 7.18e+03 1.67e+00 bond pdb=" CA LYS D 142 " pdb=" CB LYS D 142 " ideal model delta sigma weight residual 1.532 1.549 -0.017 1.33e-02 5.65e+03 1.63e+00 bond pdb=" CA LYS A 142 " pdb=" CB LYS A 142 " ideal model delta sigma weight residual 1.537 1.553 -0.016 1.31e-02 5.83e+03 1.58e+00 ... (remaining 13061 not shown) Histogram of bond angle deviations from ideal: 99.95 - 107.93: 380 107.93 - 115.90: 7848 115.90 - 123.88: 9019 123.88 - 131.86: 319 131.86 - 139.83: 15 Bond angle restraints: 17581 Sorted by residual: angle pdb=" CA ILE C 439 " pdb=" CB ILE C 439 " pdb=" CG1 ILE C 439 " ideal model delta sigma weight residual 110.40 118.76 -8.36 1.70e+00 3.46e-01 2.42e+01 angle pdb=" CA LYS A 142 " pdb=" CB LYS A 142 " pdb=" CG LYS A 142 " ideal model delta sigma weight residual 114.10 122.29 -8.19 2.00e+00 2.50e-01 1.68e+01 angle pdb=" CA LYS D 142 " pdb=" CB LYS D 142 " pdb=" CG LYS D 142 " ideal model delta sigma weight residual 114.10 121.76 -7.66 2.00e+00 2.50e-01 1.47e+01 angle pdb=" C LYS D 347 " pdb=" N TYR D 348 " pdb=" CA TYR D 348 " ideal model delta sigma weight residual 121.80 131.08 -9.28 2.44e+00 1.68e-01 1.45e+01 angle pdb=" CA GLU A 84 " pdb=" CB GLU A 84 " pdb=" CG GLU A 84 " ideal model delta sigma weight residual 114.10 121.38 -7.28 2.00e+00 2.50e-01 1.32e+01 ... (remaining 17576 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.86: 7334 17.86 - 35.72: 454 35.72 - 53.59: 108 53.59 - 71.45: 21 71.45 - 89.31: 7 Dihedral angle restraints: 7924 sinusoidal: 3266 harmonic: 4658 Sorted by residual: dihedral pdb=" CA PHE D 342 " pdb=" C PHE D 342 " pdb=" N ASP D 343 " pdb=" CA ASP D 343 " ideal model delta harmonic sigma weight residual 180.00 -163.48 -16.52 0 5.00e+00 4.00e-02 1.09e+01 dihedral pdb=" CA ALA C 236 " pdb=" C ALA C 236 " pdb=" N LEU C 237 " pdb=" CA LEU C 237 " ideal model delta harmonic sigma weight residual 180.00 164.56 15.44 0 5.00e+00 4.00e-02 9.53e+00 dihedral pdb=" CA LYS B 99 " pdb=" CB LYS B 99 " pdb=" CG LYS B 99 " pdb=" CD LYS B 99 " ideal model delta sinusoidal sigma weight residual 60.00 117.29 -57.29 3 1.50e+01 4.44e-03 9.43e+00 ... (remaining 7921 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.058: 1519 0.058 - 0.116: 349 0.116 - 0.173: 55 0.173 - 0.231: 8 0.231 - 0.289: 2 Chirality restraints: 1933 Sorted by residual: chirality pdb=" CG LEU A 11 " pdb=" CB LEU A 11 " pdb=" CD1 LEU A 11 " pdb=" CD2 LEU A 11 " both_signs ideal model delta sigma weight residual False -2.59 -2.30 -0.29 2.00e-01 2.50e+01 2.09e+00 chirality pdb=" CG LEU D 11 " pdb=" CB LEU D 11 " pdb=" CD1 LEU D 11 " pdb=" CD2 LEU D 11 " both_signs ideal model delta sigma weight residual False -2.59 -2.32 -0.27 2.00e-01 2.50e+01 1.88e+00 chirality pdb=" CB VAL B 30 " pdb=" CA VAL B 30 " pdb=" CG1 VAL B 30 " pdb=" CG2 VAL B 30 " both_signs ideal model delta sigma weight residual False -2.63 -2.40 -0.23 2.00e-01 2.50e+01 1.28e+00 ... (remaining 1930 not shown) Planarity restraints: 2242 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ILE C 439 " -0.011 2.00e-02 2.50e+03 2.28e-02 5.21e+00 pdb=" C ILE C 439 " 0.039 2.00e-02 2.50e+03 pdb=" O ILE C 439 " -0.015 2.00e-02 2.50e+03 pdb=" N SER C 440 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS A 142 " 0.012 2.00e-02 2.50e+03 2.28e-02 5.18e+00 pdb=" C LYS A 142 " -0.039 2.00e-02 2.50e+03 pdb=" O LYS A 142 " 0.014 2.00e-02 2.50e+03 pdb=" N VAL A 143 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLN A 141 " 0.009 2.00e-02 2.50e+03 1.87e-02 3.48e+00 pdb=" C GLN A 141 " -0.032 2.00e-02 2.50e+03 pdb=" O GLN A 141 " 0.012 2.00e-02 2.50e+03 pdb=" N LYS A 142 " 0.011 2.00e-02 2.50e+03 ... (remaining 2239 not shown) Histogram of nonbonded interaction distances: 2.31 - 2.82: 3657 2.82 - 3.34: 11785 3.34 - 3.86: 20568 3.86 - 4.38: 22740 4.38 - 4.90: 40035 Nonbonded interactions: 98785 Sorted by model distance: nonbonded pdb=" O GLN A 262 " pdb=" OG SER A 265 " model vdw 2.306 3.040 nonbonded pdb=" O GLN D 262 " pdb=" OG SER D 265 " model vdw 2.309 3.040 nonbonded pdb=" O GLN C 262 " pdb=" OG SER C 265 " model vdw 2.320 3.040 nonbonded pdb=" O TYR C 221 " pdb=" OG1 THR C 225 " model vdw 2.323 3.040 nonbonded pdb=" O TYR A 378 " pdb=" OG SER A 381 " model vdw 2.329 3.040 ... (remaining 98780 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 3 through 33 or resid 38 through 160 or resid 173 through \ 238 or resid 249 through 342 or resid 348 through 440)) selection = (chain 'B' and (resid 3 through 238 or resid 249 through 288 or resid 295 throug \ h 440)) selection = (chain 'C' and (resid 3 through 238 or resid 249 through 288 or resid 295 throug \ h 440)) selection = (chain 'D' and (resid 3 through 33 or resid 38 through 160 or resid 173 through \ 238 or resid 249 through 342 or resid 348 through 440)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.140 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.560 Check model and map are aligned: 0.100 Set scattering table: 0.120 Process input model: 36.590 Find NCS groups from input model: 0.630 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.800 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.000 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7782 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 13066 Z= 0.215 Angle : 0.795 11.730 17581 Z= 0.473 Chirality : 0.050 0.289 1933 Planarity : 0.005 0.046 2242 Dihedral : 12.614 89.308 4900 Min Nonbonded Distance : 2.306 Molprobity Statistics. All-atom Clashscore : 5.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.81 % Favored : 95.19 % Rotamer: Outliers : 3.08 % Allowed : 8.45 % Favored : 88.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.10 (0.22), residues: 1538 helix: 1.58 (0.18), residues: 786 sheet: -2.04 (0.30), residues: 271 loop : -1.09 (0.30), residues: 481 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 158 HIS 0.008 0.001 HIS D 32 PHE 0.022 0.002 PHE B 59 TYR 0.014 0.002 TYR B 378 ARG 0.009 0.001 ARG A 185 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3076 Ramachandran restraints generated. 1538 Oldfield, 0 Emsley, 1538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3076 Ramachandran restraints generated. 1538 Oldfield, 0 Emsley, 1538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 306 residues out of total 1398 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 263 time to evaluate : 1.388 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 55 ILE cc_start: 0.9068 (tt) cc_final: 0.8615 (tp) REVERT: A 56 ARG cc_start: 0.8285 (OUTLIER) cc_final: 0.7762 (mmm160) REVERT: A 209 GLU cc_start: 0.8485 (mm-30) cc_final: 0.8021 (tp30) REVERT: A 277 VAL cc_start: 0.9265 (m) cc_final: 0.8937 (m) REVERT: A 341 ASP cc_start: 0.7615 (t0) cc_final: 0.7103 (t0) REVERT: B 87 PHE cc_start: 0.9337 (m-80) cc_final: 0.8419 (m-80) REVERT: B 228 GLU cc_start: 0.8665 (mm-30) cc_final: 0.8447 (tm-30) REVERT: B 335 ASP cc_start: 0.8348 (m-30) cc_final: 0.8000 (t0) REVERT: B 338 MET cc_start: 0.8837 (ttt) cc_final: 0.8500 (ttt) REVERT: B 403 GLN cc_start: 0.9119 (mt0) cc_final: 0.8861 (mt0) REVERT: D 56 ARG cc_start: 0.8990 (OUTLIER) cc_final: 0.8422 (mmm160) REVERT: D 90 VAL cc_start: 0.8418 (OUTLIER) cc_final: 0.7560 (p) REVERT: D 222 GLU cc_start: 0.8402 (mm-30) cc_final: 0.8044 (tp30) REVERT: C 201 MET cc_start: 0.9009 (mmt) cc_final: 0.8724 (mmm) REVERT: C 225 THR cc_start: 0.9259 (OUTLIER) cc_final: 0.8966 (p) REVERT: C 338 MET cc_start: 0.8504 (ttp) cc_final: 0.7025 (ttp) REVERT: C 375 THR cc_start: 0.9586 (p) cc_final: 0.9334 (t) REVERT: C 414 LEU cc_start: 0.9305 (OUTLIER) cc_final: 0.9032 (mm) outliers start: 43 outliers final: 8 residues processed: 300 average time/residue: 0.2633 time to fit residues: 110.6402 Evaluate side-chains 144 residues out of total 1398 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 131 time to evaluate : 1.593 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 ARG Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain B residue 99 LYS Chi-restraints excluded: chain D residue 56 ARG Chi-restraints excluded: chain D residue 90 VAL Chi-restraints excluded: chain D residue 336 LYS Chi-restraints excluded: chain D residue 346 ARG Chi-restraints excluded: chain C residue 143 VAL Chi-restraints excluded: chain C residue 225 THR Chi-restraints excluded: chain C residue 234 PHE Chi-restraints excluded: chain C residue 235 SER Chi-restraints excluded: chain C residue 414 LEU Chi-restraints excluded: chain C residue 439 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 133 optimal weight: 20.0000 chunk 119 optimal weight: 20.0000 chunk 66 optimal weight: 6.9990 chunk 40 optimal weight: 10.0000 chunk 80 optimal weight: 1.9990 chunk 63 optimal weight: 4.9990 chunk 123 optimal weight: 9.9990 chunk 47 optimal weight: 5.9990 chunk 75 optimal weight: 2.9990 chunk 92 optimal weight: 10.0000 chunk 143 optimal weight: 8.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 94 ASN A 138 ASN A 312 GLN A 315 GLN A 399 HIS A 418 GLN B 15 HIS B 29 ASN ** B 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 85 GLN B 424 HIS D 138 ASN D 312 GLN D 315 GLN D 418 GLN C 15 HIS C 29 ASN ** C 32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 262 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7970 moved from start: 0.4000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.065 13066 Z= 0.435 Angle : 0.718 8.317 17581 Z= 0.384 Chirality : 0.044 0.165 1933 Planarity : 0.005 0.037 2242 Dihedral : 7.670 74.181 1799 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 16.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 4.51 % Allowed : 13.04 % Favored : 82.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.56 (0.22), residues: 1538 helix: 1.81 (0.18), residues: 773 sheet: -1.64 (0.29), residues: 298 loop : -0.54 (0.31), residues: 467 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A 360 HIS 0.007 0.002 HIS D 15 PHE 0.023 0.002 PHE B 332 TYR 0.021 0.002 TYR A 278 ARG 0.008 0.001 ARG B 152 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3076 Ramachandran restraints generated. 1538 Oldfield, 0 Emsley, 1538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3076 Ramachandran restraints generated. 1538 Oldfield, 0 Emsley, 1538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 1398 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 128 time to evaluate : 1.446 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 56 ARG cc_start: 0.8226 (OUTLIER) cc_final: 0.7665 (mmm160) REVERT: A 154 MET cc_start: 0.9366 (mtp) cc_final: 0.8790 (mtm) REVERT: A 209 GLU cc_start: 0.8678 (mm-30) cc_final: 0.8239 (tp30) REVERT: A 256 GLU cc_start: 0.9013 (tt0) cc_final: 0.8786 (mt-10) REVERT: A 326 MET cc_start: 0.9158 (mmt) cc_final: 0.8748 (mmm) REVERT: A 341 ASP cc_start: 0.8535 (t0) cc_final: 0.7915 (t0) REVERT: B 87 PHE cc_start: 0.9194 (m-80) cc_final: 0.8904 (m-80) REVERT: B 228 GLU cc_start: 0.8906 (mm-30) cc_final: 0.8492 (tm-30) REVERT: D 23 ASP cc_start: 0.8043 (p0) cc_final: 0.7676 (t0) REVERT: D 154 MET cc_start: 0.8726 (tmm) cc_final: 0.7478 (mtt) REVERT: D 222 GLU cc_start: 0.8576 (OUTLIER) cc_final: 0.8304 (tp30) REVERT: D 436 MET cc_start: 0.7945 (tpt) cc_final: 0.6458 (mmm) REVERT: C 326 MET cc_start: 0.9132 (mmm) cc_final: 0.8605 (mmm) REVERT: C 414 LEU cc_start: 0.9446 (OUTLIER) cc_final: 0.9207 (mm) outliers start: 63 outliers final: 26 residues processed: 184 average time/residue: 0.2434 time to fit residues: 64.9148 Evaluate side-chains 125 residues out of total 1398 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 96 time to evaluate : 1.571 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 ILE Chi-restraints excluded: chain A residue 16 ASN Chi-restraints excluded: chain A residue 56 ARG Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 104 GLU Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 226 PHE Chi-restraints excluded: chain A residue 439 ILE Chi-restraints excluded: chain B residue 28 LEU Chi-restraints excluded: chain B residue 99 LYS Chi-restraints excluded: chain B residue 428 ILE Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain D residue 8 LYS Chi-restraints excluded: chain D residue 56 ARG Chi-restraints excluded: chain D residue 222 GLU Chi-restraints excluded: chain D residue 336 LYS Chi-restraints excluded: chain D residue 346 ARG Chi-restraints excluded: chain D residue 353 LEU Chi-restraints excluded: chain D residue 354 LYS Chi-restraints excluded: chain D residue 407 LEU Chi-restraints excluded: chain C residue 14 ILE Chi-restraints excluded: chain C residue 18 TYR Chi-restraints excluded: chain C residue 98 ILE Chi-restraints excluded: chain C residue 143 VAL Chi-restraints excluded: chain C residue 153 THR Chi-restraints excluded: chain C residue 155 LEU Chi-restraints excluded: chain C residue 373 LEU Chi-restraints excluded: chain C residue 414 LEU Chi-restraints excluded: chain C residue 439 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 79 optimal weight: 10.0000 chunk 44 optimal weight: 0.7980 chunk 119 optimal weight: 20.0000 chunk 97 optimal weight: 10.0000 chunk 39 optimal weight: 1.9990 chunk 143 optimal weight: 8.9990 chunk 155 optimal weight: 6.9990 chunk 128 optimal weight: 20.0000 chunk 142 optimal weight: 5.9990 chunk 49 optimal weight: 20.0000 chunk 115 optimal weight: 7.9990 overall best weight: 4.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 48 ASN B 288 ASN ** D 15 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 94 ASN D 413 GLN ** D 424 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 32 HIS ** C 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8005 moved from start: 0.4938 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.064 13066 Z= 0.437 Angle : 0.697 9.793 17581 Z= 0.371 Chirality : 0.044 0.175 1933 Planarity : 0.004 0.033 2242 Dihedral : 6.709 72.579 1794 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 17.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % Rotamer: Outliers : 3.58 % Allowed : 15.90 % Favored : 80.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.58 (0.22), residues: 1538 helix: 1.70 (0.18), residues: 777 sheet: -1.53 (0.31), residues: 279 loop : -0.46 (0.30), residues: 482 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP A 360 HIS 0.011 0.002 HIS C 32 PHE 0.023 0.002 PHE A 230 TYR 0.026 0.002 TYR D 304 ARG 0.006 0.001 ARG B 152 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3076 Ramachandran restraints generated. 1538 Oldfield, 0 Emsley, 1538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3076 Ramachandran restraints generated. 1538 Oldfield, 0 Emsley, 1538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 1398 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 105 time to evaluate : 1.550 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 56 ARG cc_start: 0.8225 (OUTLIER) cc_final: 0.7663 (mmm160) REVERT: A 209 GLU cc_start: 0.8704 (mm-30) cc_final: 0.8250 (tp30) REVERT: A 341 ASP cc_start: 0.8567 (t0) cc_final: 0.8101 (t0) REVERT: B 87 PHE cc_start: 0.9170 (m-80) cc_final: 0.8872 (m-80) REVERT: B 151 PHE cc_start: 0.9027 (OUTLIER) cc_final: 0.8073 (p90) REVERT: D 222 GLU cc_start: 0.8626 (OUTLIER) cc_final: 0.8368 (tp30) REVERT: D 436 MET cc_start: 0.8103 (OUTLIER) cc_final: 0.6468 (mmm) REVERT: C 201 MET cc_start: 0.9132 (mmp) cc_final: 0.8910 (mmp) REVERT: C 376 MET cc_start: 0.9686 (mtm) cc_final: 0.9283 (mtp) REVERT: C 410 MET cc_start: 0.9406 (mtm) cc_final: 0.9199 (mtm) outliers start: 50 outliers final: 28 residues processed: 148 average time/residue: 0.2540 time to fit residues: 54.6726 Evaluate side-chains 121 residues out of total 1398 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 89 time to evaluate : 1.463 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 ILE Chi-restraints excluded: chain A residue 16 ASN Chi-restraints excluded: chain A residue 41 THR Chi-restraints excluded: chain A residue 56 ARG Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 104 GLU Chi-restraints excluded: chain A residue 109 VAL Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 226 PHE Chi-restraints excluded: chain A residue 439 ILE Chi-restraints excluded: chain B residue 55 ILE Chi-restraints excluded: chain B residue 98 ILE Chi-restraints excluded: chain B residue 151 PHE Chi-restraints excluded: chain B residue 152 ARG Chi-restraints excluded: chain B residue 423 THR Chi-restraints excluded: chain B residue 428 ILE Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain D residue 8 LYS Chi-restraints excluded: chain D residue 56 ARG Chi-restraints excluded: chain D residue 222 GLU Chi-restraints excluded: chain D residue 305 ARG Chi-restraints excluded: chain D residue 336 LYS Chi-restraints excluded: chain D residue 346 ARG Chi-restraints excluded: chain D residue 407 LEU Chi-restraints excluded: chain D residue 436 MET Chi-restraints excluded: chain D residue 439 ILE Chi-restraints excluded: chain C residue 18 TYR Chi-restraints excluded: chain C residue 153 THR Chi-restraints excluded: chain C residue 155 LEU Chi-restraints excluded: chain C residue 396 ILE Chi-restraints excluded: chain C residue 407 LEU Chi-restraints excluded: chain C residue 439 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 142 optimal weight: 4.9990 chunk 108 optimal weight: 5.9990 chunk 74 optimal weight: 0.8980 chunk 15 optimal weight: 2.9990 chunk 68 optimal weight: 0.7980 chunk 96 optimal weight: 1.9990 chunk 144 optimal weight: 8.9990 chunk 152 optimal weight: 3.9990 chunk 75 optimal weight: 0.9980 chunk 136 optimal weight: 6.9990 chunk 41 optimal weight: 8.9990 overall best weight: 1.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 15 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 262 GLN D 424 HIS ** C 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7938 moved from start: 0.4992 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 13066 Z= 0.183 Angle : 0.549 8.905 17581 Z= 0.292 Chirality : 0.042 0.163 1933 Planarity : 0.003 0.028 2242 Dihedral : 5.771 70.762 1787 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 11.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 2.58 % Allowed : 16.55 % Favored : 80.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.17 (0.22), residues: 1538 helix: 2.22 (0.18), residues: 774 sheet: -1.23 (0.31), residues: 279 loop : -0.24 (0.30), residues: 485 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP A 360 HIS 0.006 0.001 HIS D 15 PHE 0.013 0.001 PHE B 134 TYR 0.019 0.001 TYR D 304 ARG 0.008 0.000 ARG A 282 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3076 Ramachandran restraints generated. 1538 Oldfield, 0 Emsley, 1538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3076 Ramachandran restraints generated. 1538 Oldfield, 0 Emsley, 1538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 1398 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 100 time to evaluate : 1.605 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 56 ARG cc_start: 0.8012 (OUTLIER) cc_final: 0.7351 (mmm160) REVERT: A 209 GLU cc_start: 0.8702 (mm-30) cc_final: 0.8246 (tp30) REVERT: A 304 TYR cc_start: 0.9126 (t80) cc_final: 0.8907 (t80) REVERT: A 341 ASP cc_start: 0.8443 (t0) cc_final: 0.7883 (t0) REVERT: B 11 LEU cc_start: 0.9336 (mt) cc_final: 0.8578 (pp) REVERT: B 151 PHE cc_start: 0.8977 (OUTLIER) cc_final: 0.8214 (p90) REVERT: D 222 GLU cc_start: 0.8397 (OUTLIER) cc_final: 0.8125 (tp30) REVERT: D 304 TYR cc_start: 0.8961 (t80) cc_final: 0.8760 (t80) REVERT: D 436 MET cc_start: 0.7917 (OUTLIER) cc_final: 0.6447 (mmm) REVERT: C 187 LEU cc_start: 0.9329 (OUTLIER) cc_final: 0.9040 (mt) REVERT: C 201 MET cc_start: 0.9007 (mmp) cc_final: 0.8762 (mmm) REVERT: C 338 MET cc_start: 0.8684 (ttm) cc_final: 0.8355 (ttm) REVERT: C 376 MET cc_start: 0.9638 (mtm) cc_final: 0.9084 (mtt) REVERT: C 436 MET cc_start: 0.8957 (mpp) cc_final: 0.8479 (mpp) outliers start: 36 outliers final: 20 residues processed: 129 average time/residue: 0.2467 time to fit residues: 47.3129 Evaluate side-chains 118 residues out of total 1398 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 93 time to evaluate : 1.652 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 ARG Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 226 PHE Chi-restraints excluded: chain A residue 326 MET Chi-restraints excluded: chain A residue 407 LEU Chi-restraints excluded: chain A residue 425 SER Chi-restraints excluded: chain A residue 439 ILE Chi-restraints excluded: chain B residue 151 PHE Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 439 ILE Chi-restraints excluded: chain D residue 56 ARG Chi-restraints excluded: chain D residue 222 GLU Chi-restraints excluded: chain D residue 336 LYS Chi-restraints excluded: chain D residue 346 ARG Chi-restraints excluded: chain D residue 353 LEU Chi-restraints excluded: chain D residue 436 MET Chi-restraints excluded: chain C residue 18 TYR Chi-restraints excluded: chain C residue 49 ILE Chi-restraints excluded: chain C residue 153 THR Chi-restraints excluded: chain C residue 155 LEU Chi-restraints excluded: chain C residue 187 LEU Chi-restraints excluded: chain C residue 374 LEU Chi-restraints excluded: chain C residue 396 ILE Chi-restraints excluded: chain C residue 407 LEU Chi-restraints excluded: chain C residue 439 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 127 optimal weight: 7.9990 chunk 86 optimal weight: 7.9990 chunk 2 optimal weight: 0.9980 chunk 113 optimal weight: 20.0000 chunk 63 optimal weight: 0.9980 chunk 130 optimal weight: 10.0000 chunk 105 optimal weight: 9.9990 chunk 0 optimal weight: 3.9990 chunk 77 optimal weight: 9.9990 chunk 137 optimal weight: 0.3980 chunk 38 optimal weight: 0.4980 overall best weight: 1.3782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 15 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7931 moved from start: 0.5173 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 13066 Z= 0.175 Angle : 0.527 9.576 17581 Z= 0.279 Chirality : 0.041 0.164 1933 Planarity : 0.003 0.029 2242 Dihedral : 5.518 74.902 1787 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 11.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 2.65 % Allowed : 17.05 % Favored : 80.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.30 (0.22), residues: 1538 helix: 2.21 (0.18), residues: 783 sheet: -0.98 (0.32), residues: 279 loop : -0.14 (0.31), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 360 HIS 0.006 0.001 HIS D 15 PHE 0.013 0.001 PHE C 226 TYR 0.028 0.001 TYR A 378 ARG 0.005 0.000 ARG C 78 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3076 Ramachandran restraints generated. 1538 Oldfield, 0 Emsley, 1538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3076 Ramachandran restraints generated. 1538 Oldfield, 0 Emsley, 1538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 1398 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 99 time to evaluate : 1.552 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 56 ARG cc_start: 0.8014 (OUTLIER) cc_final: 0.7569 (mmm160) REVERT: A 209 GLU cc_start: 0.8703 (mm-30) cc_final: 0.8250 (tp30) REVERT: A 338 MET cc_start: 0.8529 (ttm) cc_final: 0.8203 (ptm) REVERT: A 341 ASP cc_start: 0.8469 (t0) cc_final: 0.7868 (t0) REVERT: B 11 LEU cc_start: 0.9349 (mt) cc_final: 0.8621 (pp) REVERT: B 151 PHE cc_start: 0.8906 (OUTLIER) cc_final: 0.8200 (p90) REVERT: B 230 PHE cc_start: 0.9131 (m-80) cc_final: 0.8828 (t80) REVERT: B 338 MET cc_start: 0.8792 (ttt) cc_final: 0.8376 (ttt) REVERT: D 436 MET cc_start: 0.7975 (OUTLIER) cc_final: 0.6522 (mmm) REVERT: C 11 LEU cc_start: 0.9658 (OUTLIER) cc_final: 0.9142 (tt) REVERT: C 187 LEU cc_start: 0.9329 (OUTLIER) cc_final: 0.9041 (mt) REVERT: C 376 MET cc_start: 0.9703 (mtm) cc_final: 0.9031 (mtt) REVERT: C 436 MET cc_start: 0.8956 (mpp) cc_final: 0.8650 (mpp) outliers start: 37 outliers final: 24 residues processed: 131 average time/residue: 0.2346 time to fit residues: 46.0879 Evaluate side-chains 123 residues out of total 1398 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 94 time to evaluate : 1.570 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 ILE Chi-restraints excluded: chain A residue 41 THR Chi-restraints excluded: chain A residue 56 ARG Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 226 PHE Chi-restraints excluded: chain A residue 407 LEU Chi-restraints excluded: chain A residue 425 SER Chi-restraints excluded: chain A residue 439 ILE Chi-restraints excluded: chain B residue 151 PHE Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 439 ILE Chi-restraints excluded: chain D residue 22 VAL Chi-restraints excluded: chain D residue 56 ARG Chi-restraints excluded: chain D residue 222 GLU Chi-restraints excluded: chain D residue 336 LYS Chi-restraints excluded: chain D residue 346 ARG Chi-restraints excluded: chain D residue 353 LEU Chi-restraints excluded: chain D residue 436 MET Chi-restraints excluded: chain C residue 11 LEU Chi-restraints excluded: chain C residue 14 ILE Chi-restraints excluded: chain C residue 18 TYR Chi-restraints excluded: chain C residue 49 ILE Chi-restraints excluded: chain C residue 155 LEU Chi-restraints excluded: chain C residue 187 LEU Chi-restraints excluded: chain C residue 373 LEU Chi-restraints excluded: chain C residue 374 LEU Chi-restraints excluded: chain C residue 396 ILE Chi-restraints excluded: chain C residue 407 LEU Chi-restraints excluded: chain C residue 439 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 51 optimal weight: 7.9990 chunk 137 optimal weight: 2.9990 chunk 30 optimal weight: 10.0000 chunk 89 optimal weight: 1.9990 chunk 37 optimal weight: 4.9990 chunk 152 optimal weight: 10.0000 chunk 126 optimal weight: 6.9990 chunk 70 optimal weight: 5.9990 chunk 12 optimal weight: 8.9990 chunk 50 optimal weight: 1.9990 chunk 80 optimal weight: 10.0000 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 286 ASN D 15 HIS D 262 GLN ** C 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7989 moved from start: 0.5647 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 13066 Z= 0.339 Angle : 0.610 9.808 17581 Z= 0.325 Chirality : 0.042 0.161 1933 Planarity : 0.004 0.034 2242 Dihedral : 6.184 82.978 1787 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 15.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.29 % Favored : 95.71 % Rotamer: Outliers : 3.44 % Allowed : 16.69 % Favored : 79.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.10 (0.22), residues: 1538 helix: 1.96 (0.18), residues: 781 sheet: -1.03 (0.33), residues: 258 loop : -0.15 (0.30), residues: 499 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP A 360 HIS 0.005 0.001 HIS D 15 PHE 0.022 0.002 PHE A 230 TYR 0.026 0.002 TYR A 378 ARG 0.006 0.001 ARG B 152 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3076 Ramachandran restraints generated. 1538 Oldfield, 0 Emsley, 1538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3076 Ramachandran restraints generated. 1538 Oldfield, 0 Emsley, 1538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 1398 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 92 time to evaluate : 1.535 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 56 ARG cc_start: 0.8202 (OUTLIER) cc_final: 0.7840 (mmm160) REVERT: A 209 GLU cc_start: 0.8712 (mm-30) cc_final: 0.8238 (tp30) REVERT: A 341 ASP cc_start: 0.8688 (t0) cc_final: 0.8155 (t0) REVERT: B 11 LEU cc_start: 0.9359 (mt) cc_final: 0.8577 (pp) REVERT: B 151 PHE cc_start: 0.8884 (OUTLIER) cc_final: 0.8121 (p90) REVERT: D 190 GLN cc_start: 0.8825 (OUTLIER) cc_final: 0.8567 (tp-100) REVERT: D 222 GLU cc_start: 0.8557 (OUTLIER) cc_final: 0.8274 (tp30) REVERT: D 424 HIS cc_start: 0.4864 (OUTLIER) cc_final: 0.4293 (t-170) REVERT: D 436 MET cc_start: 0.7958 (OUTLIER) cc_final: 0.6438 (mmm) REVERT: C 201 MET cc_start: 0.9094 (mmp) cc_final: 0.8879 (mmm) REVERT: C 376 MET cc_start: 0.9744 (mtm) cc_final: 0.9310 (mtp) outliers start: 48 outliers final: 32 residues processed: 132 average time/residue: 0.2494 time to fit residues: 48.7366 Evaluate side-chains 124 residues out of total 1398 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 86 time to evaluate : 1.554 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 ILE Chi-restraints excluded: chain A residue 16 ASN Chi-restraints excluded: chain A residue 41 THR Chi-restraints excluded: chain A residue 56 ARG Chi-restraints excluded: chain A residue 65 ILE Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 226 PHE Chi-restraints excluded: chain A residue 407 LEU Chi-restraints excluded: chain A residue 425 SER Chi-restraints excluded: chain A residue 439 ILE Chi-restraints excluded: chain B residue 151 PHE Chi-restraints excluded: chain B residue 152 ARG Chi-restraints excluded: chain B residue 423 THR Chi-restraints excluded: chain B residue 428 ILE Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 439 ILE Chi-restraints excluded: chain D residue 22 VAL Chi-restraints excluded: chain D residue 56 ARG Chi-restraints excluded: chain D residue 129 MET Chi-restraints excluded: chain D residue 178 ARG Chi-restraints excluded: chain D residue 190 GLN Chi-restraints excluded: chain D residue 222 GLU Chi-restraints excluded: chain D residue 336 LYS Chi-restraints excluded: chain D residue 346 ARG Chi-restraints excluded: chain D residue 353 LEU Chi-restraints excluded: chain D residue 424 HIS Chi-restraints excluded: chain D residue 436 MET Chi-restraints excluded: chain C residue 14 ILE Chi-restraints excluded: chain C residue 18 TYR Chi-restraints excluded: chain C residue 43 ILE Chi-restraints excluded: chain C residue 153 THR Chi-restraints excluded: chain C residue 155 LEU Chi-restraints excluded: chain C residue 373 LEU Chi-restraints excluded: chain C residue 374 LEU Chi-restraints excluded: chain C residue 396 ILE Chi-restraints excluded: chain C residue 407 LEU Chi-restraints excluded: chain C residue 410 MET Chi-restraints excluded: chain C residue 439 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 147 optimal weight: 2.9990 chunk 17 optimal weight: 0.9990 chunk 87 optimal weight: 0.0970 chunk 111 optimal weight: 9.9990 chunk 86 optimal weight: 6.9990 chunk 128 optimal weight: 9.9990 chunk 85 optimal weight: 5.9990 chunk 152 optimal weight: 9.9990 chunk 95 optimal weight: 9.9990 chunk 92 optimal weight: 1.9990 chunk 70 optimal weight: 0.9980 overall best weight: 1.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 268 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7942 moved from start: 0.5612 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 13066 Z= 0.181 Angle : 0.553 11.373 17581 Z= 0.289 Chirality : 0.041 0.160 1933 Planarity : 0.003 0.029 2242 Dihedral : 5.832 75.120 1787 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 11.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 2.87 % Allowed : 17.91 % Favored : 79.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.33 (0.22), residues: 1538 helix: 2.11 (0.18), residues: 781 sheet: -0.84 (0.33), residues: 258 loop : -0.03 (0.31), residues: 499 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A 360 HIS 0.004 0.001 HIS C 44 PHE 0.014 0.001 PHE C 226 TYR 0.021 0.001 TYR A 378 ARG 0.005 0.000 ARG B 152 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3076 Ramachandran restraints generated. 1538 Oldfield, 0 Emsley, 1538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3076 Ramachandran restraints generated. 1538 Oldfield, 0 Emsley, 1538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 1398 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 95 time to evaluate : 1.664 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 56 ARG cc_start: 0.8030 (OUTLIER) cc_final: 0.7598 (mmm160) REVERT: A 209 GLU cc_start: 0.8691 (mm-30) cc_final: 0.8233 (tp30) REVERT: A 338 MET cc_start: 0.8818 (ptm) cc_final: 0.8247 (ptm) REVERT: A 341 ASP cc_start: 0.8569 (t0) cc_final: 0.8078 (t0) REVERT: B 11 LEU cc_start: 0.9379 (mt) cc_final: 0.8678 (pp) REVERT: B 151 PHE cc_start: 0.8831 (OUTLIER) cc_final: 0.8194 (p90) REVERT: B 230 PHE cc_start: 0.9136 (m-80) cc_final: 0.8871 (t80) REVERT: D 106 MET cc_start: 0.8907 (tpt) cc_final: 0.8330 (ttt) REVERT: D 147 TYR cc_start: 0.8209 (t80) cc_final: 0.7978 (t80) REVERT: D 190 GLN cc_start: 0.8728 (OUTLIER) cc_final: 0.8474 (tp-100) REVERT: D 436 MET cc_start: 0.7927 (OUTLIER) cc_final: 0.6488 (mmm) REVERT: C 11 LEU cc_start: 0.9680 (pt) cc_final: 0.9151 (tt) REVERT: C 376 MET cc_start: 0.9724 (mtm) cc_final: 0.9016 (mtt) outliers start: 40 outliers final: 28 residues processed: 128 average time/residue: 0.2409 time to fit residues: 45.9164 Evaluate side-chains 123 residues out of total 1398 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 91 time to evaluate : 1.554 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 ILE Chi-restraints excluded: chain A residue 41 THR Chi-restraints excluded: chain A residue 56 ARG Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 226 PHE Chi-restraints excluded: chain A residue 407 LEU Chi-restraints excluded: chain A residue 423 THR Chi-restraints excluded: chain A residue 425 SER Chi-restraints excluded: chain A residue 439 ILE Chi-restraints excluded: chain B residue 151 PHE Chi-restraints excluded: chain B residue 425 SER Chi-restraints excluded: chain B residue 428 ILE Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 439 ILE Chi-restraints excluded: chain D residue 22 VAL Chi-restraints excluded: chain D residue 56 ARG Chi-restraints excluded: chain D residue 178 ARG Chi-restraints excluded: chain D residue 190 GLN Chi-restraints excluded: chain D residue 222 GLU Chi-restraints excluded: chain D residue 336 LYS Chi-restraints excluded: chain D residue 346 ARG Chi-restraints excluded: chain D residue 353 LEU Chi-restraints excluded: chain D residue 436 MET Chi-restraints excluded: chain C residue 14 ILE Chi-restraints excluded: chain C residue 18 TYR Chi-restraints excluded: chain C residue 155 LEU Chi-restraints excluded: chain C residue 373 LEU Chi-restraints excluded: chain C residue 374 LEU Chi-restraints excluded: chain C residue 396 ILE Chi-restraints excluded: chain C residue 407 LEU Chi-restraints excluded: chain C residue 410 MET Chi-restraints excluded: chain C residue 439 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 94 optimal weight: 9.9990 chunk 60 optimal weight: 4.9990 chunk 90 optimal weight: 20.0000 chunk 45 optimal weight: 0.7980 chunk 29 optimal weight: 2.9990 chunk 96 optimal weight: 5.9990 chunk 103 optimal weight: 10.0000 chunk 75 optimal weight: 2.9990 chunk 14 optimal weight: 10.0000 chunk 119 optimal weight: 20.0000 chunk 138 optimal weight: 0.7980 overall best weight: 2.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 268 ASN ** C 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7967 moved from start: 0.5796 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 13066 Z= 0.256 Angle : 0.579 11.799 17581 Z= 0.303 Chirality : 0.041 0.160 1933 Planarity : 0.003 0.029 2242 Dihedral : 6.175 78.691 1787 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 12.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 3.08 % Allowed : 17.55 % Favored : 79.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.31 (0.22), residues: 1538 helix: 2.07 (0.18), residues: 783 sheet: -0.76 (0.33), residues: 268 loop : -0.04 (0.31), residues: 487 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 360 HIS 0.002 0.001 HIS B 32 PHE 0.014 0.001 PHE C 226 TYR 0.018 0.001 TYR A 378 ARG 0.007 0.000 ARG B 152 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3076 Ramachandran restraints generated. 1538 Oldfield, 0 Emsley, 1538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3076 Ramachandran restraints generated. 1538 Oldfield, 0 Emsley, 1538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 1398 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 90 time to evaluate : 1.551 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 56 ARG cc_start: 0.8106 (OUTLIER) cc_final: 0.7482 (mmm160) REVERT: A 209 GLU cc_start: 0.8706 (mm-30) cc_final: 0.8253 (tp30) REVERT: A 338 MET cc_start: 0.8828 (ptm) cc_final: 0.8011 (ptm) REVERT: A 341 ASP cc_start: 0.8689 (t0) cc_final: 0.8196 (t0) REVERT: B 11 LEU cc_start: 0.9385 (mt) cc_final: 0.8680 (pp) REVERT: B 151 PHE cc_start: 0.8831 (OUTLIER) cc_final: 0.7974 (p90) REVERT: B 230 PHE cc_start: 0.9165 (m-80) cc_final: 0.8896 (t80) REVERT: D 190 GLN cc_start: 0.8787 (OUTLIER) cc_final: 0.8508 (tp-100) REVERT: D 222 GLU cc_start: 0.8538 (OUTLIER) cc_final: 0.8242 (tp30) REVERT: D 424 HIS cc_start: 0.4833 (OUTLIER) cc_final: 0.4178 (t-170) REVERT: D 436 MET cc_start: 0.7910 (OUTLIER) cc_final: 0.6437 (mmm) REVERT: C 11 LEU cc_start: 0.9677 (pt) cc_final: 0.9146 (tt) REVERT: C 187 LEU cc_start: 0.9357 (OUTLIER) cc_final: 0.9037 (mt) REVERT: C 326 MET cc_start: 0.9165 (mmm) cc_final: 0.8195 (mmm) REVERT: C 376 MET cc_start: 0.9738 (mtm) cc_final: 0.9276 (mtp) outliers start: 43 outliers final: 27 residues processed: 125 average time/residue: 0.2401 time to fit residues: 44.8429 Evaluate side-chains 124 residues out of total 1398 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 90 time to evaluate : 1.544 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 ILE Chi-restraints excluded: chain A residue 41 THR Chi-restraints excluded: chain A residue 56 ARG Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 226 PHE Chi-restraints excluded: chain A residue 423 THR Chi-restraints excluded: chain A residue 425 SER Chi-restraints excluded: chain A residue 439 ILE Chi-restraints excluded: chain B residue 151 PHE Chi-restraints excluded: chain B residue 425 SER Chi-restraints excluded: chain B residue 428 ILE Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 439 ILE Chi-restraints excluded: chain D residue 22 VAL Chi-restraints excluded: chain D residue 56 ARG Chi-restraints excluded: chain D residue 178 ARG Chi-restraints excluded: chain D residue 190 GLN Chi-restraints excluded: chain D residue 222 GLU Chi-restraints excluded: chain D residue 336 LYS Chi-restraints excluded: chain D residue 346 ARG Chi-restraints excluded: chain D residue 353 LEU Chi-restraints excluded: chain D residue 424 HIS Chi-restraints excluded: chain D residue 436 MET Chi-restraints excluded: chain C residue 14 ILE Chi-restraints excluded: chain C residue 18 TYR Chi-restraints excluded: chain C residue 43 ILE Chi-restraints excluded: chain C residue 153 THR Chi-restraints excluded: chain C residue 155 LEU Chi-restraints excluded: chain C residue 187 LEU Chi-restraints excluded: chain C residue 373 LEU Chi-restraints excluded: chain C residue 374 LEU Chi-restraints excluded: chain C residue 396 ILE Chi-restraints excluded: chain C residue 410 MET Chi-restraints excluded: chain C residue 439 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 145 optimal weight: 4.9990 chunk 133 optimal weight: 8.9990 chunk 141 optimal weight: 9.9990 chunk 85 optimal weight: 3.9990 chunk 61 optimal weight: 9.9990 chunk 111 optimal weight: 6.9990 chunk 43 optimal weight: 7.9990 chunk 128 optimal weight: 6.9990 chunk 134 optimal weight: 4.9990 chunk 93 optimal weight: 10.0000 chunk 150 optimal weight: 10.0000 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8026 moved from start: 0.6375 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.077 13066 Z= 0.507 Angle : 0.768 11.558 17581 Z= 0.403 Chirality : 0.045 0.178 1933 Planarity : 0.004 0.047 2242 Dihedral : 6.610 82.926 1787 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 18.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.27 % Favored : 94.73 % Rotamer: Outliers : 3.51 % Allowed : 17.98 % Favored : 78.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.52 (0.22), residues: 1538 helix: 1.31 (0.18), residues: 795 sheet: -1.20 (0.31), residues: 276 loop : -0.12 (0.33), residues: 467 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP A 360 HIS 0.006 0.001 HIS B 32 PHE 0.019 0.002 PHE D 230 TYR 0.038 0.002 TYR C 432 ARG 0.010 0.001 ARG B 152 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3076 Ramachandran restraints generated. 1538 Oldfield, 0 Emsley, 1538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3076 Ramachandran restraints generated. 1538 Oldfield, 0 Emsley, 1538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 1398 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 87 time to evaluate : 1.554 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 209 GLU cc_start: 0.8749 (mm-30) cc_final: 0.8262 (tp30) REVERT: A 338 MET cc_start: 0.8897 (ptm) cc_final: 0.8238 (ptm) REVERT: A 341 ASP cc_start: 0.8849 (t0) cc_final: 0.8457 (t0) REVERT: B 151 PHE cc_start: 0.8864 (OUTLIER) cc_final: 0.8163 (p90) REVERT: B 230 PHE cc_start: 0.9234 (OUTLIER) cc_final: 0.8900 (t80) REVERT: D 190 GLN cc_start: 0.8864 (OUTLIER) cc_final: 0.8476 (tp-100) REVERT: D 222 GLU cc_start: 0.8647 (OUTLIER) cc_final: 0.8280 (tt0) REVERT: D 424 HIS cc_start: 0.4331 (OUTLIER) cc_final: 0.3846 (t-170) REVERT: C 376 MET cc_start: 0.9776 (mtm) cc_final: 0.9320 (mtp) outliers start: 49 outliers final: 34 residues processed: 128 average time/residue: 0.2432 time to fit residues: 46.0104 Evaluate side-chains 124 residues out of total 1398 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 85 time to evaluate : 1.560 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 ILE Chi-restraints excluded: chain A residue 9 ILE Chi-restraints excluded: chain A residue 16 ASN Chi-restraints excluded: chain A residue 41 THR Chi-restraints excluded: chain A residue 65 ILE Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 226 PHE Chi-restraints excluded: chain A residue 326 MET Chi-restraints excluded: chain A residue 407 LEU Chi-restraints excluded: chain A residue 423 THR Chi-restraints excluded: chain A residue 425 SER Chi-restraints excluded: chain A residue 439 ILE Chi-restraints excluded: chain B residue 151 PHE Chi-restraints excluded: chain B residue 152 ARG Chi-restraints excluded: chain B residue 230 PHE Chi-restraints excluded: chain B residue 423 THR Chi-restraints excluded: chain B residue 425 SER Chi-restraints excluded: chain B residue 428 ILE Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 439 ILE Chi-restraints excluded: chain D residue 56 ARG Chi-restraints excluded: chain D residue 178 ARG Chi-restraints excluded: chain D residue 190 GLN Chi-restraints excluded: chain D residue 222 GLU Chi-restraints excluded: chain D residue 336 LYS Chi-restraints excluded: chain D residue 346 ARG Chi-restraints excluded: chain D residue 353 LEU Chi-restraints excluded: chain D residue 354 LYS Chi-restraints excluded: chain D residue 424 HIS Chi-restraints excluded: chain C residue 14 ILE Chi-restraints excluded: chain C residue 18 TYR Chi-restraints excluded: chain C residue 43 ILE Chi-restraints excluded: chain C residue 97 TYR Chi-restraints excluded: chain C residue 153 THR Chi-restraints excluded: chain C residue 155 LEU Chi-restraints excluded: chain C residue 373 LEU Chi-restraints excluded: chain C residue 374 LEU Chi-restraints excluded: chain C residue 396 ILE Chi-restraints excluded: chain C residue 439 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 91 optimal weight: 7.9990 chunk 71 optimal weight: 0.5980 chunk 104 optimal weight: 6.9990 chunk 157 optimal weight: 0.0570 chunk 144 optimal weight: 2.9990 chunk 125 optimal weight: 0.8980 chunk 13 optimal weight: 0.7980 chunk 96 optimal weight: 0.9990 chunk 76 optimal weight: 0.9980 chunk 99 optimal weight: 9.9990 chunk 133 optimal weight: 8.9990 overall best weight: 0.6698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 372 GLN ** C 44 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7929 moved from start: 0.6080 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 13066 Z= 0.157 Angle : 0.601 12.724 17581 Z= 0.310 Chirality : 0.043 0.176 1933 Planarity : 0.003 0.030 2242 Dihedral : 5.911 71.204 1783 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 11.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 2.01 % Allowed : 19.70 % Favored : 78.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.22 (0.23), residues: 1538 helix: 1.97 (0.18), residues: 783 sheet: -0.91 (0.32), residues: 268 loop : 0.06 (0.32), residues: 487 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP A 360 HIS 0.005 0.001 HIS B 32 PHE 0.022 0.001 PHE D 183 TYR 0.018 0.001 TYR A 378 ARG 0.006 0.000 ARG B 152 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3076 Ramachandran restraints generated. 1538 Oldfield, 0 Emsley, 1538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3076 Ramachandran restraints generated. 1538 Oldfield, 0 Emsley, 1538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 1398 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 98 time to evaluate : 1.532 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 209 GLU cc_start: 0.8700 (mm-30) cc_final: 0.8260 (tp30) REVERT: A 338 MET cc_start: 0.8802 (ptm) cc_final: 0.8412 (ptm) REVERT: A 341 ASP cc_start: 0.8561 (t0) cc_final: 0.8061 (t0) REVERT: B 11 LEU cc_start: 0.9318 (mt) cc_final: 0.8671 (pp) REVERT: B 230 PHE cc_start: 0.9085 (OUTLIER) cc_final: 0.8854 (t80) REVERT: D 190 GLN cc_start: 0.8712 (OUTLIER) cc_final: 0.8445 (tp-100) REVERT: D 222 GLU cc_start: 0.8474 (OUTLIER) cc_final: 0.8218 (tp30) REVERT: D 424 HIS cc_start: 0.4593 (OUTLIER) cc_final: 0.4260 (t-170) REVERT: D 436 MET cc_start: 0.8069 (tpt) cc_final: 0.6633 (mmm) REVERT: C 11 LEU cc_start: 0.9669 (pt) cc_final: 0.9105 (tt) REVERT: C 187 LEU cc_start: 0.9329 (OUTLIER) cc_final: 0.9006 (mt) REVERT: C 376 MET cc_start: 0.9749 (mtm) cc_final: 0.8998 (mtt) outliers start: 28 outliers final: 19 residues processed: 122 average time/residue: 0.2122 time to fit residues: 40.0756 Evaluate side-chains 113 residues out of total 1398 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 89 time to evaluate : 1.607 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 ILE Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 226 PHE Chi-restraints excluded: chain A residue 423 THR Chi-restraints excluded: chain A residue 425 SER Chi-restraints excluded: chain A residue 439 ILE Chi-restraints excluded: chain B residue 97 TYR Chi-restraints excluded: chain B residue 151 PHE Chi-restraints excluded: chain B residue 230 PHE Chi-restraints excluded: chain B residue 425 SER Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain D residue 56 ARG Chi-restraints excluded: chain D residue 190 GLN Chi-restraints excluded: chain D residue 222 GLU Chi-restraints excluded: chain D residue 336 LYS Chi-restraints excluded: chain D residue 346 ARG Chi-restraints excluded: chain D residue 424 HIS Chi-restraints excluded: chain C residue 14 ILE Chi-restraints excluded: chain C residue 18 TYR Chi-restraints excluded: chain C residue 97 TYR Chi-restraints excluded: chain C residue 187 LEU Chi-restraints excluded: chain C residue 373 LEU Chi-restraints excluded: chain C residue 396 ILE Chi-restraints excluded: chain C residue 439 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 38 optimal weight: 0.0000 chunk 115 optimal weight: 0.9980 chunk 18 optimal weight: 7.9990 chunk 34 optimal weight: 4.9990 chunk 125 optimal weight: 10.0000 chunk 52 optimal weight: 2.9990 chunk 128 optimal weight: 0.8980 chunk 15 optimal weight: 9.9990 chunk 23 optimal weight: 4.9990 chunk 110 optimal weight: 8.9990 chunk 7 optimal weight: 5.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3801 r_free = 0.3801 target = 0.070895 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.049052 restraints weight = 70522.095| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.050850 restraints weight = 33940.482| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.051903 restraints weight = 22265.279| |-----------------------------------------------------------------------------| r_work (final): 0.3217 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8131 moved from start: 0.6177 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 13066 Z= 0.223 Angle : 0.618 12.245 17581 Z= 0.318 Chirality : 0.042 0.205 1933 Planarity : 0.003 0.029 2242 Dihedral : 5.964 77.153 1783 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 13.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 1.79 % Allowed : 20.27 % Favored : 77.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.25 (0.23), residues: 1538 helix: 1.94 (0.18), residues: 788 sheet: -0.81 (0.32), residues: 270 loop : 0.11 (0.32), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP A 360 HIS 0.004 0.001 HIS C 44 PHE 0.023 0.001 PHE D 183 TYR 0.018 0.001 TYR A 278 ARG 0.004 0.000 ARG C 78 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2422.64 seconds wall clock time: 44 minutes 16.39 seconds (2656.39 seconds total)